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        Class&nbsp;Aligner
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Aligner</h1><p class="nomargin-top"></p>
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<p>Aligner is the class that creates sequence or structure 
  alignments.</p>

<!-- ==================== NESTED CLASSES ==================== -->
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      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk._moltk.Aligner.Cell-class.html" class="summary-name">Cell</a><br />
      An Aligner::Cell is one node in the dynamic programming table
    </td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk._moltk.Aligner.QueryPosition-class.html" class="summary-name">QueryPosition</a><br />
      Aligner::Position represents a special biosequence residue that 
        knows how to score itself during alignment.
    </td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk._moltk.Aligner.Scorer-class.html" class="summary-name">Scorer</a><br />
      Aligner::Scorer converts dumb sequence and structure residues into 
        Aligner::Positions, which know how to quickly score themselves with
        other AlignerPositions.
    </td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk._moltk.Aligner.Stage-class.html" class="summary-name">Stage</a>
    </td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk._moltk.Aligner.TargetPosition-class.html" class="summary-name">TargetPosition</a>
    </td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk._moltk.Aligner.TracebackPointer-class.html" class="summary-name">TracebackPointer</a>
    </td>
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<!-- ==================== INSTANCE METHODS ==================== -->
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      <span class="summary-type">&nbsp;</span>
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          <td><span class="summary-sig"><a href="moltk._moltk.Aligner-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">...</span>)</span><br />
      __init__( (object)arg1) -&gt; None :</td>
          <td align="right" valign="top">
            
            
          </td>
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      </table>
      
    </td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk._moltk.Aligner-class.html#__reduce__" class="summary-sig-name">__reduce__</a>(<span class="summary-sig-arg">...</span>)</span><br />
      helper for pickle</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
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<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk._moltk.Aligner-class.html#align" class="summary-sig-name">align</a>(<span class="summary-sig-arg">...</span>)</span><br />
      align( (Aligner)arg1, (Alignment)arg0, (Alignment)arg1) -&gt; Alignment :</td>
          <td align="right" valign="top">
            
            
          </td>
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    </td>
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<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk._moltk.Aligner-class.html#get_end_gaps_free" class="summary-sig-name">get_end_gaps_free</a>(<span class="summary-sig-arg">...</span>)</span><br />
      get_end_gaps_free( (Aligner)arg1) -&gt; bool :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
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    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk._moltk.Aligner-class.html#set_end_gaps_free" class="summary-sig-name">set_end_gaps_free</a>(<span class="summary-sig-arg">...</span>)</span><br />
      set_end_gaps_free( (Aligner)arg1, (bool)f) -&gt; None :</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
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  <tr>
    <td colspan="2" class="summary">
    <p class="indent-wrapped-lines"><b>Inherited from <code><i>unreachable</i>.instance</code></b>:
      <code>__new__</code>
      </p>
    <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
      <code>__delattr__</code>,
      <code>__format__</code>,
      <code>__getattribute__</code>,
      <code>__hash__</code>,
      <code>__reduce_ex__</code>,
      <code>__repr__</code>,
      <code>__setattr__</code>,
      <code>__sizeof__</code>,
      <code>__str__</code>,
      <code>__subclasshook__</code>
      </p>
    </td>
  </tr>
</table>
<!-- ==================== STATIC METHODS ==================== -->
<a name="section-StaticMethods"></a>
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       cellspacing="0" width="100%" bgcolor="white">
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        <td align="left"><span class="table-header">Static Methods</span></td>
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         ><span class="options">[<a href="#section-StaticMethods"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
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  </td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">Scorer :</span>
    </td><td class="summary">
      <table width="100%" cellpadding="0" cellspacing="0" border="0">
        <tr>
          <td><span class="summary-sig"><a href="moltk._moltk.Aligner-class.html#get_default_scorer" class="summary-sig-name">get_default_scorer</a>()</span><br />
      C++ signature :...</td>
          <td align="right" valign="top">
            
            
          </td>
        </tr>
      </table>
      
    </td>
  </tr>
</table>
<!-- ==================== CLASS VARIABLES ==================== -->
<a name="section-ClassVariables"></a>
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        <td align="left"><span class="table-header">Class Variables</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-ClassVariables"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
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    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="STAGE_ALLOCATED"></a><span class="summary-name">STAGE_ALLOCATED</span> = <code title="moltk._moltk.Stage.STAGE_ALLOCATED">moltk._moltk.Stage.STAGE_ALLOCATED</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="STAGE_EMPTY"></a><span class="summary-name">STAGE_EMPTY</span> = <code title="moltk._moltk.Stage.STAGE_EMPTY">moltk._moltk.Stage.STAGE_EMPTY</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk._moltk.Aligner-class.html#STAGE_RECURRENCE_COMPUTED" class="summary-name">STAGE_RECURRENCE_COMPUTED</a> = <code title="moltk._moltk.Stage.STAGE_RECURRENCE_COMPUTED">moltk._moltk.Stage.STAGE_RECURRENC<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="STAGE_SCORER"></a><span class="summary-name">STAGE_SCORER</span> = <code title="moltk._moltk.Stage.STAGE_SCORER">moltk._moltk.Stage.STAGE_SCORER</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="STAGE_SEQUENCE"></a><span class="summary-name">STAGE_SEQUENCE</span> = <code title="moltk._moltk.Stage.STAGE_SEQUENCE">moltk._moltk.Stage.STAGE_SEQUENCE</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk._moltk.Aligner-class.html#STAGE_TABLE_INITIALIZED" class="summary-name">STAGE_TABLE_INITIALIZED</a> = <code title="moltk._moltk.Stage.STAGE_TABLE_INITIALIZED">moltk._moltk.Stage.STAGE_TABLE_INITI<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="STAGE_TRACED"></a><span class="summary-name">STAGE_TRACED</span> = <code title="moltk._moltk.Stage.STAGE_TRACED">moltk._moltk.Stage.STAGE_TRACED</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="TRACEBACK_DONE"></a><span class="summary-name">TRACEBACK_DONE</span> = <code title="moltk._moltk.TracebackPointer.TRACEBACK_DONE">moltk._moltk.TracebackPointer.TRACEBACK_DONE</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="TRACEBACK_LEFT"></a><span class="summary-name">TRACEBACK_LEFT</span> = <code title="moltk._moltk.TracebackPointer.TRACEBACK_LEFT">moltk._moltk.TracebackPointer.TRACEBACK_LEFT</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk._moltk.Aligner-class.html#TRACEBACK_NOT_INITIALIZED" class="summary-name">TRACEBACK_NOT_INITIALIZED</a> = <code title="moltk._moltk.TracebackPointer.TRACEBACK_NOT_INITIALIZED">moltk._moltk.TracebackPointer.TRAC<code class="variable-ellipsis">...</code></code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="TRACEBACK_UP"></a><span class="summary-name">TRACEBACK_UP</span> = <code title="moltk._moltk.TracebackPointer.TRACEBACK_UP">moltk._moltk.TracebackPointer.TRACEBACK_UP</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="TRACEBACK_UPLEFT"></a><span class="summary-name">TRACEBACK_UPLEFT</span> = <code title="moltk._moltk.TracebackPointer.TRACEBACK_UPLEFT">moltk._moltk.TracebackPointer.TRACEBACK_UPLEFT</code>
    </td>
  </tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a name="__instance_size__"></a><span class="summary-name">__instance_size__</span> = <code title="376">376</code>
    </td>
  </tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Properties</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-Properties"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
      </tr>
    </table>
  </td>
</tr>
<tr>
    <td width="15%" align="right" valign="top" class="summary">
      <span class="summary-type">&nbsp;</span>
    </td><td class="summary">
        <a href="moltk._moltk.Aligner-class.html#endGapsFree" class="summary-name">endGapsFree</a>
    </td>
  </tr>
  <tr>
    <td colspan="2" class="summary">
    <p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
      <code>__class__</code>
      </p>
    </td>
  </tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
  <td colspan="2" class="table-header">
    <table border="0" cellpadding="0" cellspacing="0" width="100%">
      <tr valign="top">
        <td align="left"><span class="table-header">Method Details</span></td>
        <td align="right" valign="top"
         ><span class="options">[<a href="#section-MethodDetails"
         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
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<a name="__init__"></a>
<div>
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       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">...</span>)</span>
    <br /><em class="fname">(Constructor)</em>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

__init__( (object)arg1) -&gt; None :

    C++ signature :
        void __init__(_object*)

</pre>
  <dl class="fields">
    <dt>Overrides:
        object.__init__
    </dt>
  </dl>
</td></tr></table>
</div>
<a name="__reduce__"></a>
<div>
<table class="details" border="1" cellpadding="3"
       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">__reduce__</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <p>helper for pickle</p>
  <dl class="fields">
    <dt>Overrides:
        object.__reduce__
        <dd><em class="note">(inherited documentation)</em></dd>
    </dt>
  </dl>
</td></tr></table>
</div>
<a name="align"></a>
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       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">align</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

align( (Aligner)arg1, (Alignment)arg0, (Alignment)arg1) -&gt; Alignment :

    C++ signature :
        moltk::Alignment align(moltk::Aligner {lvalue},moltk::Alignment,moltk::Alignment)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="get_default_scorer"></a>
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       cellspacing="0" width="100%" bgcolor="white">
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  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">get_default_scorer</span>()</span>
    <br /><em class="fname">Static Method</em>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">
    C++ signature :
        moltk::Aligner::Scorer get_default_scorer()

</pre>
  <dl class="fields">
    <dt>Returns: Scorer :</dt>
  </dl>
</td></tr></table>
</div>
<a name="get_end_gaps_free"></a>
<div>
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       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">get_end_gaps_free</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

get_end_gaps_free( (Aligner)arg1) -&gt; bool :

    C++ signature :
        bool get_end_gaps_free(moltk::Aligner {lvalue})

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<a name="set_end_gaps_free"></a>
<div>
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       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <table width="100%" cellpadding="0" cellspacing="0" border="0">
  <tr valign="top"><td>
  <h3 class="epydoc"><span class="sig"><span class="sig-name">set_end_gaps_free</span>(<span class="sig-arg">...</span>)</span>
  </h3>
  </td><td align="right" valign="top"
    >&nbsp;
    </td>
  </tr></table>
  
  <pre class="literalblock">

set_end_gaps_free( (Aligner)arg1, (bool)f) -&gt; None :

    C++ signature :
        void set_end_gaps_free(moltk::Aligner {lvalue},bool)

</pre>
  <dl class="fields">
  </dl>
</td></tr></table>
</div>
<br />
<!-- ==================== CLASS VARIABLE DETAILS ==================== -->
<a name="section-ClassVariableDetails"></a>
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         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
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<a name="STAGE_RECURRENCE_COMPUTED"></a>
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  <h3 class="epydoc">STAGE_RECURRENCE_COMPUTED</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
moltk._moltk.Stage.STAGE_RECURRENCE_COMPUTED
</pre></td></tr></table>
</dd>
  </dl>
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<a name="STAGE_TABLE_INITIALIZED"></a>
<div>
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       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">STAGE_TABLE_INITIALIZED</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
moltk._moltk.Stage.STAGE_TABLE_INITIALIZED
</pre></td></tr></table>
</dd>
  </dl>
</td></tr></table>
</div>
<a name="TRACEBACK_NOT_INITIALIZED"></a>
<div>
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       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">TRACEBACK_NOT_INITIALIZED</h3>
  
  <dl class="fields">
  </dl>
  <dl class="fields">
    <dt>Value:</dt>
      <dd><table><tr><td><pre class="variable">
moltk._moltk.TracebackPointer.TRACEBACK_NOT_INITIALIZED
</pre></td></tr></table>
</dd>
  </dl>
</td></tr></table>
</div>
<br />
<!-- ==================== PROPERTY DETAILS ==================== -->
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         class="privatelink" onclick="toggle_private();"
         >hide private</a>]</span></td>
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<a name="endGapsFree"></a>
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       cellspacing="0" width="100%" bgcolor="white">
<tr><td>
  <h3 class="epydoc">endGapsFree</h3>
  
  <dl class="fields">
    <dt>Get Method:</dt>
    <dd class="value"><span class="summary-sig"><i>unreachable</i>(<span class="summary-sig-arg">...</span>)</span>
    </dd>
    <dt>Set Method:</dt>
    <dd class="value"><span class="summary-sig"><i>unreachable</i>(<span class="summary-sig-arg">...</span>)</span>
    </dd>
  </dl>
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